Arsenic (As) in the aquatic environment is a considerable environmental issue, previous studies have reported the toxic effects of low concentrations (≤ 150 μg/L) of As on fish. However, limited information is available regarding the impact of low levels of As on apoptosis. To evaluate this, zebrafish embryos were exposed to different concentrations (0, 25, 50, 75, and 150 μg/L) of As (arsenite AsIII and arsenate AsV) for 120 h. Our results indicated that low concentrations of AsIII exposure significantly inhibited the survival of zebrafish larvae, and significantly increased the transcription of Caspase-9 and Caspase-3, the ratio of Bax/Bcl-2 transcription, and protein levels of Caspase-3. In contrast, AsV decreased the ratios of Bax/Bcl-2 transcription and protein levels, as well as protein levels of Caspase-3. Our data demonstrated that AsIII and AsV exert different toxic effects, AsIII induced apoptosis via the mitochondrial pathway and the extrinsic pathway, while AsV induced apoptosis only via the mitochondrial pathway. •Our study focused on the impact of low concentrations of arsenic on the apoptotic toxicity and manner of zebrafish larvae.•Low concentration of arsenite decreased the survival rate of zebrafish larvae, while low concentration arsenate had no effect on it.•Low concentration of arsenite can induce apoptosis of zebrafish larvae stage via the mitochondrial pathway and the extrinsic pathway.•Low concentration of arsenate can induce apoptosis of zebrafish larvae stage via the mitochondrial pathway.